We've put together the necessary information to run your medical, dental, and vision insurance through Gusto.

Note: COBRA health insurance premium payments obtained from a previous W-2 employer can not be run through the S-Corp and reported in Gusto.

Click here to get educated on healthcare in general and how to obtain a plan.

Why are we running insurance through payroll?

Why aren't COBRA premiums eligible for the self-employed (SE) health insurance deduction?

Are premiums paid to a healthcare sharing ministry eligible for the self-employed (SE) health insurance deduction?

How do I set up my health insurance in Gusto?

How will I make my insurance payments?

How do I need to map the accounts in Gusto so it syncs correctly with QuickBooks/Xero?

How will my premiums be reported in my books?

What if I have premiums paid that are not reported in Gusto?


Why are we running insurance through payroll?

For reporting purposes, health insurance premiums (excluding COBRA premiums) paid on behalf of a greater than 2% S-corp shareholder-employee are deductible by the S-corp and reportable as wages on the shareholder-employees Form W-2, subject to income tax withholding.

However, these additional wages are not subject to Social Security, Medicare (FICA), or Unemployment (FUTA) taxes if the payments of premiums are made to or on behalf of an employee under a plan or system that makes provision for all or a class of employees (or employees and their dependents). Therefore, the additional compensation is included in the shareholder-employee’s Box 1 (Wages) of Form W-2, Wage and Tax Statement, but is not included in Boxes 3 and 5 of Form W-2.

Sources: IRS: S Corp Compensation Medical Insurance


Why aren't COBRA premiums eligible for the self-employed (SE) health insurance deduction?

COBRA premiums are not eligible for the SE health insurance deduction because eligible health insurance policies must either be in the name of the S-corp or the owner of the S-Corp. COBRA is a continuation of a prior employer’s plan therefore the policy is in the employer’s name making it ineligible for that deduction. The COBRA premiums can be taken on your personal tax return (Form 1040) as an itemized deduction but certain thresholds need to be met to receive a benefit. Premiums are not to be ran in Gusto.


Are premiums paid to a healthcare sharing ministry eligible for the self-employed (SE) health insurance deduction?

Yes! In the past, the IRS did not consider healthcare sharing ministry plans eligible health insurance and therefore premiums were not deductible. Proposed regulations were made in 2020 to consider these new sharing plans health insurance similar to traditional insurance plans. We believe these regulations will be formally approved and are comfortable allowing members to consider these premiums eligible for the SE health insurance deduction. Premiums should be ran in Gusto just like other traditional insurance premiums.


How do I set up my health insurance in Gusto?

To get this done, you need to know the monthly premium. To add in Gusto, go to the "Benefits" tab (far left menu) > scroll down to "All Benefits" section > Select "Medical, Dental, & Vision" under the "Health" heading.

  • Select Yes — we currently offer this benefit

  • Select "I'll Manage Benefits Myself"

  • Input Benefit Name (Keep it generic: ex. Kaiser Medical Insurance)

  • Input Health Benefit Type (Medical, Dental, or Vision)

  • Employee deduction per pay period: Enter $0.00 (zero must be entered)

  • Company Contribution per pay period: Enter the premium per pay period

    • If payroll is ran monthly: input 100% of monthly premium

    • If payroll is ran 2x/month: input 50% of monthly premium

    • If payroll is ran every other week: Calculate monthly premium * 12/26

    • If payroll is ran weekly: Calculate monthly premium * 12/52


How will I make my insurance payments?

You’ll make the payments to your benefits provider from your business checking or credit card account. Gusto does not remit payment to 3rd-Party benefits providers, so please ensure you make these payments yourself. Payments from your business checking or credit card should be applied to the Payroll Liabilities account in your accounting software.


How do I need to map the accounts in Gusto so it syncs correctly with QuickBooks/Xero?

Once the benefit is set up in Gusto, go to the App Directory > Connected Apps > QuickBooks > Edit > All to setup the mapping to QuickBooks/Xero.

Mapping for expenses

Mapping for liabilities

If either of these accounts are not listed, please reach out to us and we can get them added.


How will my premiums be reported in my books?

The information in Gusto will be automatically synced to QuickBooks/Xero. The Gusto entry will treat the premiums as an expense on your P&L and also an amount to be paid on your balance sheet (Payroll Liabilities). The payments of the premiums are then categorized as a Payroll Liability to zero out the balance due.


What if I have premiums paid that are not reported in Gusto?

Email [email protected] and your Accounting Advisor can help make any updates or corrections.


Have any other questions?

Reach out to the Collective team at [email protected] 😉

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